Mercurial > repos > greg > cfsan_snp_pipeline_merge_vcfs
changeset 0:e958c5f7c9d1 draft
Uploaded
| author | greg |
|---|---|
| date | Wed, 22 Nov 2023 15:34:14 +0000 |
| parents | |
| children | ab24883161d3 |
| files | .shed.yml cfsan_snp_pipeline_merge_vcfs.xml macros.xml snp_wind.py test-data/output.vcf test-data/output2.vcf test-data/samples/sample1/consensus.vcf test-data/samples/sample2/consensus.vcf test-data/samples/sample3/consensus.vcf test-data/samples/sample4/consensus.vcf |
| diffstat | 8 files changed, 884 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Wed Nov 22 15:34:14 2023 +0000 @@ -0,0 +1,9 @@ +name: cfsan_snp_pipeline_merge_vcfs +owner: greg +description: Merge the consensus vcf files from all samples into a single multi-vcf file. +long_description: Merge the consensus vcf files from all samples into a single multi-vcf file +categories: +- Metagenomics +remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/snp_pipeline/cfsan_snp_pipeline_merge_vcfs +homepage_url: https://github.com/gregvonkuster/galaxy_tools +type: unrestricted
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cfsan_snp_pipeline_merge_vcfs.xml Wed Nov 22 15:34:14 2023 +0000 @@ -0,0 +1,56 @@ +<tool id="cfsan_snp_pipeline_merge_vcfs" name="CFSAN SNP Pipeline: merge vcfs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>from multiple samples</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +python '$__tool_directory__/snp_wind.py' ./ +#if str($input_type_cond.input_type) == 'single': + -n '$input_vcf.element_identifier' + -f '$input_vcf' +#else: + #for $input_vcf in $input_vcf_collection + -n '$input_vcf.element_identifier' + -f '$input_vcf' + #end for +#end if +-p 'consensus.vcf' > ./file +&& cfsan_snp_pipeline merge_vcfs ./file + ]]></command> + <inputs> + <expand macro="input_type_cond"/> + </inputs> + <outputs> + <data name="output" format="vcf"/> + </outputs> + <tests> + <test> + <param name="input_type" value="collection"/> + <param name="input_vcf_collection"> + <collection type="list"> + <element name="sample1" value="samples/sample1/consensus.vcf" ftype="vcf"/> + <element name="sample2" value="samples/sample2/consensus.vcf" ftype="vcf"/> + <element name="sample3" value="samples/sample3/consensus.vcf" ftype="vcf"/> + <element name="sample4" value="samples/sample4/consensus.vcf" ftype="vcf"/> + </collection> + </param> + <output name="output" ftype="vcf"> + <assert_contents> + <has_size value="0" delta="100"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +**What it does** + +Merges the consensus vcf files from all samples into a single multi-vcf file. + +**More information** + +CFSAN SNP Pipeline `merge sites documentation <https://snp-pipeline.readthedocs.io/en/latest/cmd_ref.html#merge-sites>`_ + ]]></help> + <expand macro="citations"/> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Nov 22 15:34:14 2023 +0000 @@ -0,0 +1,33 @@ +<macros> + <token name="@TOOL_VERSION@">2.2.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">21.01</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.18">bcftools</requirement> + <requirement type="package" version="3.11.5">python</requirement> + <requirement type="package" version="@TOOL_VERSION@">snp-pipeline</requirement> + <requirement type="package" version="1.11">tabix</requirement> + </requirements> + </xml> + <xml name="input_type_cond"> + <conditional name="input_type_cond"> + <param name="input_type" type="select" label="Choose the category for the files to be analyzed"> + <option value="single" selected="true">Single files</option> + <option value="collection">Collection of files</option> + </param> + <when value="single"> + <param name="input_vcf" type="data" format="vcf" label="VCF file"/> + </when> + <when value="collection"> + <param name="input_vcf_collection" type="data_collection" format="vcf" collection_type="list" label="Collection of VCF files"/> + </when> + </conditional> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.7717/peerj-cs.20</citation> + </citations> + </xml> +</macros> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snp_wind.py Wed Nov 22 15:34:14 2023 +0000 @@ -0,0 +1,42 @@ +#!/usr/bin/env python + +import argparse +import os +from os.path import join as j +from itertools import zip_longest + + +def setup(base_dir, names=[], fwds=[], revs=[], extension='vcf', pattern="{name}.{orient}.{ext}"): + if fwds and revs and names and len(fwds) != len(revs) != len(names): + raise ValueError('number of forward reads must equal number of reverse reads and names') + elif len(fwds) != len(names) or not fwds or not names: + raise ValueError('number of forward reads must equal number of names') + with open(j(base_dir, 'snp-unwind.sh'), 'w') as unwind: + for i, (name, fwd, rev) in enumerate(zip_longest(names, fwds, revs)): + dir = j(base_dir, str(i)) + sample_dir = j(dir, name) + os.makedirs(sample_dir) + target_f = j(sample_dir, pattern.format(name=name, orient=1, ext=extension)) + if rev: + target_r = j(sample_dir, pattern.format(name=name, orient=2, ext=extension)) + os.symlink(fwd, target_f) + if rev: + os.symlink(rev, target_r) + print(sample_dir) + if rev: + unwind.write('unlink {}\n'.format(target_r)) + unwind.write('unlink {}\n'.format(target_f)) + unwind.write('rmdir {}\n'.format(sample_dir)) + unwind.write('rmdir {}\n'.format(dir)) + + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description="set up vcf symlink directories for snp-pipeline") + parser.add_argument('base_dir') + parser.add_argument('-n', dest='names', type=str, action='append', default=[]) + parser.add_argument('-f', dest='fwds', type=str, action='append', default=[]) + parser.add_argument('-r', dest='revs', type=str, action='append', default=[]) + parser.add_argument('-e', dest='extension', default='vcf') + parser.add_argument('-p', dest='pattern', default='{name}.{orient}.{ext}') + params = parser.parse_args() + setup(**vars(params))
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samples/sample1/consensus.vcf Wed Nov 22 15:34:14 2023 +0000 @@ -0,0 +1,186 @@ +##fileformat=VCFv4.1 +##fileDate=20180103 +##source=CFSAN SNP-Pipeline 1.0.1 +##reference=lambda_virus.fasta +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw read depth"> +##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)"> +##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)"> +##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)"> +##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)"> +##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)"> +##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)"> +##FORMAT=<ID=FT,Number=1,Type=String,Description="Genotype filters using the same codes as the FILTER data element"> +##FILTER=<ID=PASS,Description="All filters passed"> +##FILTER=<ID=RawDpth,Description="No read depth"> +##FILTER=<ID=VarFreq60,Description="Variant base frequency below 0.60"> +##FILTER=<ID=StrDpth0,Description="Less than 0 variant-supporing reads on at least one strand"> +##FILTER=<ID=StrBias0,Description="Fraction of variant supporting reads below 0.00 on one strand"> +##FILTER=<ID=Region,Description="Position is in dense region of snps or near the end of the contig."> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 +gi|9626243|ref|NC_001416.1| 403 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:27:0:27:0:0:13:14:PASS +gi|9626243|ref|NC_001416.1| 550 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:21:1:13:8:0:1:PASS +gi|9626243|ref|NC_001416.1| 586 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:18:0:12:6:0:0:PASS +gi|9626243|ref|NC_001416.1| 753 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:24:0:0:16:8:PASS +gi|9626243|ref|NC_001416.1| 1019 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:10:15:0:0:PASS +gi|9626243|ref|NC_001416.1| 1079 . T C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:26:0:25:0:0:9:16:PASS +gi|9626243|ref|NC_001416.1| 1540 . A G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:24:0:24:0:0:13:11:PASS +gi|9626243|ref|NC_001416.1| 1620 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:31:31:0:14:17:0:0:PASS +gi|9626243|ref|NC_001416.1| 1650 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:31:31:0:14:17:0:0:PASS +gi|9626243|ref|NC_001416.1| 1788 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:10:14:0:0:PASS +gi|9626243|ref|NC_001416.1| 1804 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:23:0:23:0:0:11:12:PASS +gi|9626243|ref|NC_001416.1| 2123 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:24:0:24:0:0:11:13:PASS +gi|9626243|ref|NC_001416.1| 2439 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:13:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 2452 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:18:1:9:9:0:1:PASS +gi|9626243|ref|NC_001416.1| 2599 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:28:28:0:16:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 3063 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:16:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 3351 . C G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:24:0:24:0:0:10:14:PASS +gi|9626243|ref|NC_001416.1| 3648 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:13:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 3656 . T G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:25:0:0:13:12:PASS +gi|9626243|ref|NC_001416.1| 3678 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:17:17:0:7:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 4977 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:25:0:0:12:13:PASS +gi|9626243|ref|NC_001416.1| 5142 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:21:3:11:10:3:0:PASS +gi|9626243|ref|NC_001416.1| 5336 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:12:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 5462 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:14:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 5482 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:18:0:18:0:0:9:9:PASS +gi|9626243|ref|NC_001416.1| 5516 . T A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:16:0:16:0:0:9:7:PASS +gi|9626243|ref|NC_001416.1| 5800 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:19:0:19:0:0:5:14:PASS +gi|9626243|ref|NC_001416.1| 5818 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:10:15:0:0:PASS +gi|9626243|ref|NC_001416.1| 5994 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:15:15:0:6:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 6296 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:19:0:11:8:0:0:PASS +gi|9626243|ref|NC_001416.1| 6535 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:15:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 6824 . A C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:19:0:19:0:0:11:8:PASS +gi|9626243|ref|NC_001416.1| 7424 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:20:19:1:8:11:0:1:PASS +gi|9626243|ref|NC_001416.1| 7668 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:27:26:1:17:9:0:1:PASS +gi|9626243|ref|NC_001416.1| 7897 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:26:0:26:0:0:13:13:PASS +gi|9626243|ref|NC_001416.1| 8420 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:31:31:0:19:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 8938 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:13:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 9175 . A G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:22:0:22:0:0:8:14:PASS +gi|9626243|ref|NC_001416.1| 9234 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:22:1:12:10:0:1:PASS +gi|9626243|ref|NC_001416.1| 9919 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:32:32:0:16:16:0:0:PASS +gi|9626243|ref|NC_001416.1| 10127 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:25:1:13:12:0:1:PASS +gi|9626243|ref|NC_001416.1| 10264 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:30:30:0:20:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 10421 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:16:16:0:7:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 10568 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:22:1:14:8:0:1:PASS +gi|9626243|ref|NC_001416.1| 11066 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:23:1:12:11:0:1:PASS +gi|9626243|ref|NC_001416.1| 11128 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:13:13:0:7:6:0:0:PASS +gi|9626243|ref|NC_001416.1| 11782 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:15:7:0:0:PASS +gi|9626243|ref|NC_001416.1| 12070 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:16:2:7:9:2:0:PASS +gi|9626243|ref|NC_001416.1| 12717 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:29:0:28:0:0:13:15:PASS +gi|9626243|ref|NC_001416.1| 12795 . C T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:27:0:27:0:0:17:10:PASS +gi|9626243|ref|NC_001416.1| 12876 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:29:29:0:17:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 12959 . T G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:22:0:22:0:0:14:8:PASS +gi|9626243|ref|NC_001416.1| 12970 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:19:0:9:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 13107 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:17:1:7:10:0:1:PASS +gi|9626243|ref|NC_001416.1| 13264 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:16:15:1:7:8:1:0:PASS +gi|9626243|ref|NC_001416.1| 13542 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:13:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 13647 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:20:1:8:12:0:1:PASS +gi|9626243|ref|NC_001416.1| 13952 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:9:17:0:0:PASS +gi|9626243|ref|NC_001416.1| 13971 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:17:1:8:9:0:1:PASS +gi|9626243|ref|NC_001416.1| 15384 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:24:1:17:7:1:0:PASS +gi|9626243|ref|NC_001416.1| 15715 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:19:0:8:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 15967 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:10:10:0:10:0:0:0:PASS +gi|9626243|ref|NC_001416.1| 16070 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:12:12:0:9:3:0:0:PASS +gi|9626243|ref|NC_001416.1| 16654 . C G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:24:0:24:0:0:15:9:PASS +gi|9626243|ref|NC_001416.1| 16715 . T G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:19:0:19:0:0:9:10:PASS +gi|9626243|ref|NC_001416.1| 17142 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:17:17:0:10:7:0:0:PASS +gi|9626243|ref|NC_001416.1| 17311 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:15:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 17854 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:10:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 18151 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:18:0:9:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 18188 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:11:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 18210 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:19:0:12:7:0:0:PASS +gi|9626243|ref|NC_001416.1| 18420 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:11:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 18598 . C G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:25:0:0:14:11:PASS +gi|9626243|ref|NC_001416.1| 18652 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:12:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 18989 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:32:32:0:12:20:0:0:PASS +gi|9626243|ref|NC_001416.1| 19208 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:10:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 19448 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:17:17:0:7:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 19469 . G T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:21:0:21:0:0:11:10:PASS +gi|9626243|ref|NC_001416.1| 20079 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:14:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 20099 . C T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:28:0:28:0:0:14:14:PASS +gi|9626243|ref|NC_001416.1| 20289 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:32:31:1:15:16:1:0:PASS +gi|9626243|ref|NC_001416.1| 20367 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:29:29:0:9:20:0:0:PASS +gi|9626243|ref|NC_001416.1| 21110 . T G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:18:0:18:0:0:6:12:PASS +gi|9626243|ref|NC_001416.1| 21320 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:12:14:0:0:PASS +gi|9626243|ref|NC_001416.1| 21653 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:24:1:10:14:1:0:PASS +gi|9626243|ref|NC_001416.1| 22220 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:10:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 22357 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:18:0:10:8:0:0:PASS +gi|9626243|ref|NC_001416.1| 22747 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:11:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 23362 . T A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:14:0:14:0:0:5:9:PASS +gi|9626243|ref|NC_001416.1| 23457 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:28:28:0:10:18:0:0:PASS +gi|9626243|ref|NC_001416.1| 24043 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:25:1:11:14:1:0:PASS +gi|9626243|ref|NC_001416.1| 24319 . G T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:19:0:19:0:0:7:12:PASS +gi|9626243|ref|NC_001416.1| 24766 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:19:0:19:0:0:8:11:PASS +gi|9626243|ref|NC_001416.1| 24930 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:20:1:10:10:1:0:PASS +gi|9626243|ref|NC_001416.1| 25005 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:20:1:11:9:1:0:PASS +gi|9626243|ref|NC_001416.1| 25158 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:21:1:10:11:1:0:PASS +gi|9626243|ref|NC_001416.1| 25645 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:16:16:0:7:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 26173 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:18:1:8:10:1:0:PASS +gi|9626243|ref|NC_001416.1| 26728 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:15:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 26972 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:20:6:0:0:PASS +gi|9626243|ref|NC_001416.1| 27412 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:8:17:0:0:PASS +gi|9626243|ref|NC_001416.1| 27539 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:29:29:0:16:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 27661 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:14:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 27722 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:9:16:0:0:PASS +gi|9626243|ref|NC_001416.1| 27790 . A C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:20:0:19:0:0:8:11:PASS +gi|9626243|ref|NC_001416.1| 27825 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:13:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 27834 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:16:15:1:4:11:0:1:PASS +gi|9626243|ref|NC_001416.1| 28045 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:24:2:15:9:0:2:PASS +gi|9626243|ref|NC_001416.1| 28362 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:8:17:0:0:PASS +gi|9626243|ref|NC_001416.1| 29265 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:13:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 29411 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:28:28:0:18:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 29435 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:33:33:0:16:17:0:0:PASS +gi|9626243|ref|NC_001416.1| 29891 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:21:0:21:0:0:9:12:PASS +gi|9626243|ref|NC_001416.1| 30125 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:20:20:0:11:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 30757 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:23:1:8:15:1:0:PASS +gi|9626243|ref|NC_001416.1| 30890 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:28:28:0:12:16:0:0:PASS +gi|9626243|ref|NC_001416.1| 31328 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:15:14:1:7:7:0:1:PASS +gi|9626243|ref|NC_001416.1| 31363 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:12:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 31551 . A G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:16:0:16:0:0:8:8:PASS +gi|9626243|ref|NC_001416.1| 32086 . T A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:17:1:16:1:0:7:9:PASS +gi|9626243|ref|NC_001416.1| 32660 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:14:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 33000 . C T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:18:0:18:0:0:8:10:PASS +gi|9626243|ref|NC_001416.1| 33591 . T G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:30:0:30:0:0:16:14:PASS +gi|9626243|ref|NC_001416.1| 33612 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:29:29:0:14:15:0:0:PASS +gi|9626243|ref|NC_001416.1| 33865 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:12:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 34137 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:27:27:0:13:14:0:0:PASS +gi|9626243|ref|NC_001416.1| 34370 . A G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:23:0:22:0:0:10:12:PASS +gi|9626243|ref|NC_001416.1| 34812 . A C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:16:0:15:0:0:11:4:PASS +gi|9626243|ref|NC_001416.1| 34920 . T C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:16:0:16:0:0:9:7:PASS +gi|9626243|ref|NC_001416.1| 35148 . C A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:16:0:16:0:0:10:6:PASS +gi|9626243|ref|NC_001416.1| 35802 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:19:0:5:14:0:0:PASS +gi|9626243|ref|NC_001416.1| 35907 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:16:16:0:1:15:0:0:PASS +gi|9626243|ref|NC_001416.1| 36010 . C T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:9:0:9:0:0:0:9:PASS +gi|9626243|ref|NC_001416.1| 36169 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:6:6:0:4:2:0:0:PASS +gi|9626243|ref|NC_001416.1| 36642 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:15:15:0:2:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 37208 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:19:0:19:0:0:8:11:PASS +gi|9626243|ref|NC_001416.1| 37387 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:12:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 37519 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:20:2:8:12:2:0:PASS +gi|9626243|ref|NC_001416.1| 37898 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:18:0:10:8:0:0:PASS +gi|9626243|ref|NC_001416.1| 38073 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:11:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 38165 . T C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:29:0:29:0:0:19:10:PASS +gi|9626243|ref|NC_001416.1| 38575 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:14:13:1:7:6:1:0:PASS +gi|9626243|ref|NC_001416.1| 39003 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:9:8:1:8:0:1:0:PASS +gi|9626243|ref|NC_001416.1| 39206 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:12:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 39484 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:13:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 39485 . A C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:20:0:20:0:0:10:10:PASS +gi|9626243|ref|NC_001416.1| 40457 . T C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:28:1:27:1:0:11:16:PASS +gi|9626243|ref|NC_001416.1| 40835 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:18:0:11:7:0:0:PASS +gi|9626243|ref|NC_001416.1| 40984 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:12:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 41064 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:14:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 41448 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:34:34:0:14:20:0:0:PASS +gi|9626243|ref|NC_001416.1| 41954 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:13:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 42439 . A C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:28:0:28:0:0:20:8:PASS +gi|9626243|ref|NC_001416.1| 43306 . T G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:33:0:32:0:0:12:20:PASS +gi|9626243|ref|NC_001416.1| 43470 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:23:1:12:11:0:1:PASS +gi|9626243|ref|NC_001416.1| 44134 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:28:28:0:14:14:0:0:PASS +gi|9626243|ref|NC_001416.1| 44201 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:28:28:0:12:16:0:0:PASS +gi|9626243|ref|NC_001416.1| 44413 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:29:29:0:15:14:0:0:PASS +gi|9626243|ref|NC_001416.1| 45364 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:31:31:0:18:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 45409 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:30:30:0:19:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 46237 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:27:0:27:0:0:12:15:PASS +gi|9626243|ref|NC_001416.1| 46283 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:11:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 46842 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:17:1:4:13:0:1:PASS +gi|9626243|ref|NC_001416.1| 47425 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:12:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 47893 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:28:0:28:0:0:12:16:PASS
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samples/sample2/consensus.vcf Wed Nov 22 15:34:14 2023 +0000 @@ -0,0 +1,186 @@ +##fileformat=VCFv4.1 +##fileDate=20180103 +##source=CFSAN SNP-Pipeline 1.0.1 +##reference=lambda_virus.fasta +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw read depth"> +##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)"> +##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)"> +##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)"> +##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)"> +##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)"> +##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)"> +##FORMAT=<ID=FT,Number=1,Type=String,Description="Genotype filters using the same codes as the FILTER data element"> +##FILTER=<ID=PASS,Description="All filters passed"> +##FILTER=<ID=RawDpth,Description="No read depth"> +##FILTER=<ID=VarFreq60,Description="Variant base frequency below 0.60"> +##FILTER=<ID=StrDpth0,Description="Less than 0 variant-supporing reads on at least one strand"> +##FILTER=<ID=StrBias0,Description="Fraction of variant supporting reads below 0.00 on one strand"> +##FILTER=<ID=Region,Description="Position is in dense region of snps or near the end of the contig."> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample2 +gi|9626243|ref|NC_001416.1| 403 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:11:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 550 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:14:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 586 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:12:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 753 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:27:27:0:10:17:0:0:PASS +gi|9626243|ref|NC_001416.1| 1019 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:18:0:7:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 1079 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:20:20:0:10:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 1540 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:3:19:0:0:PASS +gi|9626243|ref|NC_001416.1| 1620 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:11:10:1:0:10:0:1:PASS +gi|9626243|ref|NC_001416.1| 1650 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:9:9:0:0:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 1788 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:8:8:0:8:0:0:0:PASS +gi|9626243|ref|NC_001416.1| 1804 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:11:11:0:10:1:0:0:PASS +gi|9626243|ref|NC_001416.1| 2123 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:20:20:0:10:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 2439 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:16:16:0:10:6:0:0:PASS +gi|9626243|ref|NC_001416.1| 2452 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:21:1:11:10:1:0:PASS +gi|9626243|ref|NC_001416.1| 2599 . C A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:25:0:0:8:17:PASS +gi|9626243|ref|NC_001416.1| 3063 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:25:1:16:9:0:1:PASS +gi|9626243|ref|NC_001416.1| 3351 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:31:30:1:12:18:0:1:PASS +gi|9626243|ref|NC_001416.1| 3648 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:10:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 3656 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:20:20:0:8:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 3678 . C T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:19:1:18:1:0:10:8:PASS +gi|9626243|ref|NC_001416.1| 4977 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:30:29:1:12:17:1:0:PASS +gi|9626243|ref|NC_001416.1| 5142 . C G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:18:0:18:0:0:4:14:PASS +gi|9626243|ref|NC_001416.1| 5336 . G T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:8:0:8:0:0:1:7:PASS +gi|9626243|ref|NC_001416.1| 5462 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:9:9:0:9:0:0:0:PASS +gi|9626243|ref|NC_001416.1| 5482 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:12:10:2:10:0:2:0:PASS +gi|9626243|ref|NC_001416.1| 5516 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:11:10:1:10:0:1:0:PASS +gi|9626243|ref|NC_001416.1| 5800 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:16:7:0:0:PASS +gi|9626243|ref|NC_001416.1| 5818 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:15:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 5994 . A T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:21:0:21:0:0:10:11:PASS +gi|9626243|ref|NC_001416.1| 6296 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:10:14:0:0:PASS +gi|9626243|ref|NC_001416.1| 6535 . C A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:22:0:21:0:0:8:13:PASS +gi|9626243|ref|NC_001416.1| 6824 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:23:1:8:15:1:0:PASS +gi|9626243|ref|NC_001416.1| 7424 . G T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:24:0:0:15:9:PASS +gi|9626243|ref|NC_001416.1| 7668 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:14:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 7897 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:9:17:0:0:PASS +gi|9626243|ref|NC_001416.1| 8420 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:11:15:0:0:PASS +gi|9626243|ref|NC_001416.1| 8938 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:12:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 9175 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:13:12:1:3:9:0:1:PASS +gi|9626243|ref|NC_001416.1| 9234 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:10:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 9919 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:19:0:8:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 10127 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:32:0:32:0:0:17:15:PASS +gi|9626243|ref|NC_001416.1| 10264 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:10:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 10421 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:30:30:0:22:8:0:0:PASS +gi|9626243|ref|NC_001416.1| 10568 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:11:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 11066 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:11:15:0:0:PASS +gi|9626243|ref|NC_001416.1| 11128 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:28:28:0:11:17:0:0:PASS +gi|9626243|ref|NC_001416.1| 11782 . A G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:17:0:17:0:0:7:10:PASS +gi|9626243|ref|NC_001416.1| 12070 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:20:20:0:9:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 12717 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:7:15:0:0:PASS +gi|9626243|ref|NC_001416.1| 12795 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:11:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 12876 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:14:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 12959 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:19:0:8:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 12970 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:20:20:0:9:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 13107 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:20:1:7:13:1:0:PASS +gi|9626243|ref|NC_001416.1| 13264 . C T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:23:0:23:0:0:15:8:PASS +gi|9626243|ref|NC_001416.1| 13542 . C G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:26:0:25:0:0:16:9:PASS +gi|9626243|ref|NC_001416.1| 13647 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:27:27:0:15:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 13952 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:33:0:33:0:0:14:19:PASS +gi|9626243|ref|NC_001416.1| 13971 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:28:28:0:13:15:0:0:PASS +gi|9626243|ref|NC_001416.1| 15384 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:30:30:0:14:16:0:0:PASS +gi|9626243|ref|NC_001416.1| 15715 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:24:0:24:0:0:17:7:PASS +gi|9626243|ref|NC_001416.1| 15967 . A T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:28:0:26:0:0:14:12:PASS +gi|9626243|ref|NC_001416.1| 16070 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:27:27:0:19:8:0:0:PASS +gi|9626243|ref|NC_001416.1| 16654 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:20:20:0:8:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 16715 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:27:27:0:14:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 17142 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:27:0:27:0:0:14:13:PASS +gi|9626243|ref|NC_001416.1| 17311 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:35:0:35:0:0:15:20:PASS +gi|9626243|ref|NC_001416.1| 17854 . G T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:20:0:20:0:0:6:14:PASS +gi|9626243|ref|NC_001416.1| 18151 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:27:27:0:16:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 18188 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:31:31:0:14:17:0:0:PASS +gi|9626243|ref|NC_001416.1| 18210 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:30:28:2:13:15:0:2:PASS +gi|9626243|ref|NC_001416.1| 18420 . G T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:18:0:18:0:0:10:8:PASS +gi|9626243|ref|NC_001416.1| 18598 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:28:27:1:14:13:0:1:PASS +gi|9626243|ref|NC_001416.1| 18652 . G T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:25:0:0:15:10:PASS +gi|9626243|ref|NC_001416.1| 18989 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:15:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 19208 . A C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:17:0:17:0:0:9:8:PASS +gi|9626243|ref|NC_001416.1| 19448 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:32:32:0:14:18:0:0:PASS +gi|9626243|ref|NC_001416.1| 19469 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:30:30:0:12:18:0:0:PASS +gi|9626243|ref|NC_001416.1| 20079 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:14:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 20099 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:28:28:0:16:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 20289 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:34:34:0:19:15:0:0:PASS +gi|9626243|ref|NC_001416.1| 20367 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:32:0:32:0:0:20:12:PASS +gi|9626243|ref|NC_001416.1| 21110 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:31:31:0:20:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 21320 . T C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:25:0:0:12:13:PASS +gi|9626243|ref|NC_001416.1| 21653 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:22:1:8:14:1:0:PASS +gi|9626243|ref|NC_001416.1| 22220 . A C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:28:0:28:0:0:17:11:PASS +gi|9626243|ref|NC_001416.1| 22357 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:17:17:0:6:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 22747 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:19:0:19:0:0:7:12:PASS +gi|9626243|ref|NC_001416.1| 23362 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:20:1:9:11:1:0:PASS +gi|9626243|ref|NC_001416.1| 23457 . A C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:20:0:19:0:0:12:7:PASS +gi|9626243|ref|NC_001416.1| 24043 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:12:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 24319 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:20:1:9:11:1:0:PASS +gi|9626243|ref|NC_001416.1| 24766 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:19:0:7:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 24930 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:15:15:0:8:7:0:0:PASS +gi|9626243|ref|NC_001416.1| 25005 . A C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:12:0:12:0:0:6:6:PASS +gi|9626243|ref|NC_001416.1| 25158 . A C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:22:0:22:0:0:11:11:PASS +gi|9626243|ref|NC_001416.1| 25645 . C G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:26:0:26:0:0:11:15:PASS +gi|9626243|ref|NC_001416.1| 26173 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:21:0:21:0:0:10:11:PASS +gi|9626243|ref|NC_001416.1| 26728 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:28:28:0:12:16:0:0:PASS +gi|9626243|ref|NC_001416.1| 26972 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:25:1:11:14:1:0:PASS +gi|9626243|ref|NC_001416.1| 27412 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:13:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 27539 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:31:31:0:13:18:0:0:PASS +gi|9626243|ref|NC_001416.1| 27661 . T C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:24:0:0:14:10:PASS +gi|9626243|ref|NC_001416.1| 27722 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:30:29:1:12:17:1:0:PASS +gi|9626243|ref|NC_001416.1| 27790 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:27:26:1:13:13:1:0:PASS +gi|9626243|ref|NC_001416.1| 27825 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:14:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 27834 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:32:32:0:18:14:0:0:PASS +gi|9626243|ref|NC_001416.1| 28045 . G T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:25:0:0:13:12:PASS +gi|9626243|ref|NC_001416.1| 28362 . T C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:22:0:22:0:0:12:10:PASS +gi|9626243|ref|NC_001416.1| 29265 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:13:8:0:0:PASS +gi|9626243|ref|NC_001416.1| 29411 . T C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:31:0:31:0:0:15:16:PASS +gi|9626243|ref|NC_001416.1| 29435 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:29:27:2:12:15:1:1:PASS +gi|9626243|ref|NC_001416.1| 29891 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:19:0:10:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 30125 . A G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:21:0:21:0:0:11:10:PASS +gi|9626243|ref|NC_001416.1| 30757 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:9:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 30890 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:11:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 31328 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:11:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 31363 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:10:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 31551 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:10:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 32086 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:25:1:10:15:0:1:PASS +gi|9626243|ref|NC_001416.1| 32660 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:20:1:12:8:1:0:PASS +gi|9626243|ref|NC_001416.1| 33000 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:15:14:1:10:4:1:0:PASS +gi|9626243|ref|NC_001416.1| 33591 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:25:1:11:14:1:0:PASS +gi|9626243|ref|NC_001416.1| 33612 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:24:1:8:16:1:0:PASS +gi|9626243|ref|NC_001416.1| 33865 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:11:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 34137 . T G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:34:0:33:0:0:18:15:PASS +gi|9626243|ref|NC_001416.1| 34370 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:31:31:0:12:19:0:0:PASS +gi|9626243|ref|NC_001416.1| 34812 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:18:0:7:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 34920 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:12:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 35148 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:28:28:0:13:15:0:0:PASS +gi|9626243|ref|NC_001416.1| 35802 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:15:8:0:0:PASS +gi|9626243|ref|NC_001416.1| 35907 . G T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:32:0:30:0:0:19:11:PASS +gi|9626243|ref|NC_001416.1| 36010 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:28:28:0:12:16:0:0:PASS +gi|9626243|ref|NC_001416.1| 36169 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:29:28:1:15:13:0:1:PASS +gi|9626243|ref|NC_001416.1| 36642 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:14:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 37208 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:19:7:0:0:PASS +gi|9626243|ref|NC_001416.1| 37387 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:29:29:0:13:16:0:0:PASS +gi|9626243|ref|NC_001416.1| 37519 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:19:0:10:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 37898 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:29:28:1:14:14:1:0:PASS +gi|9626243|ref|NC_001416.1| 38073 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:27:26:1:15:11:0:1:PASS +gi|9626243|ref|NC_001416.1| 38165 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:18:1:14:4:0:1:PASS +gi|9626243|ref|NC_001416.1| 38575 . A C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:21:0:21:0:0:10:11:PASS +gi|9626243|ref|NC_001416.1| 39003 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:16:16:0:6:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 39206 . T C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:20:0:19:0:0:7:12:PASS +gi|9626243|ref|NC_001416.1| 39484 . C A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:20:0:20:0:0:12:8:PASS +gi|9626243|ref|NC_001416.1| 39485 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:14:7:0:0:PASS +gi|9626243|ref|NC_001416.1| 40457 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:32:31:1:15:16:1:0:PASS +gi|9626243|ref|NC_001416.1| 40835 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:33:33:0:17:16:0:0:PASS +gi|9626243|ref|NC_001416.1| 40984 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:19:0:7:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 41064 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:31:31:0:17:14:0:0:PASS +gi|9626243|ref|NC_001416.1| 41448 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:12:14:0:0:PASS +gi|9626243|ref|NC_001416.1| 41954 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:32:32:0:16:16:0:0:PASS +gi|9626243|ref|NC_001416.1| 42439 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:13:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 43306 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:29:29:0:13:16:0:0:PASS +gi|9626243|ref|NC_001416.1| 43470 . G T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:25:0:0:14:11:PASS +gi|9626243|ref|NC_001416.1| 44134 . T C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:22:0:21:0:0:12:9:PASS +gi|9626243|ref|NC_001416.1| 44201 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:30:30:0:13:17:0:0:PASS +gi|9626243|ref|NC_001416.1| 44413 . G T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:32:0:32:0:0:13:19:PASS +gi|9626243|ref|NC_001416.1| 45364 . A C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:27:0:25:0:0:16:9:PASS +gi|9626243|ref|NC_001416.1| 45409 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:13:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 46237 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:19:0:3:16:0:0:PASS +gi|9626243|ref|NC_001416.1| 46283 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:12:12:0:1:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 46842 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:29:28:1:12:16:1:0:PASS +gi|9626243|ref|NC_001416.1| 47425 . T C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:19:0:18:0:0:11:7:PASS +gi|9626243|ref|NC_001416.1| 47893 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:11:11:0:5:6:0:0:PASS
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samples/sample3/consensus.vcf Wed Nov 22 15:34:14 2023 +0000 @@ -0,0 +1,186 @@ +##fileformat=VCFv4.1 +##fileDate=20180103 +##source=CFSAN SNP-Pipeline 1.0.1 +##reference=lambda_virus.fasta +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw read depth"> +##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)"> +##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)"> +##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)"> +##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)"> +##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)"> +##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)"> +##FORMAT=<ID=FT,Number=1,Type=String,Description="Genotype filters using the same codes as the FILTER data element"> +##FILTER=<ID=PASS,Description="All filters passed"> +##FILTER=<ID=RawDpth,Description="No read depth"> +##FILTER=<ID=VarFreq60,Description="Variant base frequency below 0.60"> +##FILTER=<ID=StrDpth0,Description="Less than 0 variant-supporing reads on at least one strand"> +##FILTER=<ID=StrBias0,Description="Fraction of variant supporting reads below 0.00 on one strand"> +##FILTER=<ID=Region,Description="Position is in dense region of snps or near the end of the contig."> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample3 +gi|9626243|ref|NC_001416.1| 403 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:13:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 550 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:29:29:0:13:16:0:0:PASS +gi|9626243|ref|NC_001416.1| 586 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:37:37:0:15:22:0:0:PASS +gi|9626243|ref|NC_001416.1| 753 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:24:2:13:11:0:2:PASS +gi|9626243|ref|NC_001416.1| 1019 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:10:15:0:0:PASS +gi|9626243|ref|NC_001416.1| 1079 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:31:30:1:16:14:1:0:PASS +gi|9626243|ref|NC_001416.1| 1540 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:10:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 1620 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:10:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 1650 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:11:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 1788 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:13:13:0:3:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 1804 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:14:14:0:7:7:0:0:PASS +gi|9626243|ref|NC_001416.1| 2123 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:10:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 2439 . C T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:16:0:16:0:0:8:8:PASS +gi|9626243|ref|NC_001416.1| 2452 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:20:1:10:10:0:1:PASS +gi|9626243|ref|NC_001416.1| 2599 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:12:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 3063 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:24:1:11:13:0:1:PASS +gi|9626243|ref|NC_001416.1| 3351 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:29:29:0:15:14:0:0:PASS +gi|9626243|ref|NC_001416.1| 3648 . C T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:28:0:27:0:0:15:12:PASS +gi|9626243|ref|NC_001416.1| 3656 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:12:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 3678 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:15:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 4977 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:27:27:0:11:16:0:0:PASS +gi|9626243|ref|NC_001416.1| 5142 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:12:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 5336 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:17:1:11:6:1:0:PASS +gi|9626243|ref|NC_001416.1| 5462 . C T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:24:0:22:0:0:17:5:PASS +gi|9626243|ref|NC_001416.1| 5482 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:14:8:0:0:PASS +gi|9626243|ref|NC_001416.1| 5516 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:19:0:11:8:0:0:PASS +gi|9626243|ref|NC_001416.1| 5800 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:10:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 5818 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:21:1:10:11:1:0:PASS +gi|9626243|ref|NC_001416.1| 5994 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:9:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 6296 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:11:14:0:0:PASS +gi|9626243|ref|NC_001416.1| 6535 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:19:0:7:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 6824 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:14:13:1:5:8:0:1:PASS +gi|9626243|ref|NC_001416.1| 7424 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:29:28:1:11:17:0:1:PASS +gi|9626243|ref|NC_001416.1| 7668 . A C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:17:0:17:0:0:6:11:PASS +gi|9626243|ref|NC_001416.1| 7897 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:13:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 8420 . T C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:32:0:32:0:0:22:10:PASS +gi|9626243|ref|NC_001416.1| 8938 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:29:29:0:19:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 9175 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:15:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 9234 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:27:27:0:11:16:0:0:PASS +gi|9626243|ref|NC_001416.1| 9919 . A G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:24:0:24:0:0:14:10:PASS +gi|9626243|ref|NC_001416.1| 10127 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:14:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 10264 . G T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:24:0:24:0:0:10:14:PASS +gi|9626243|ref|NC_001416.1| 10421 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:16:14:2:6:8:2:0:PASS +gi|9626243|ref|NC_001416.1| 10568 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:16:16:0:9:7:0:0:PASS +gi|9626243|ref|NC_001416.1| 11066 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:20:0:20:0:0:6:14:PASS +gi|9626243|ref|NC_001416.1| 11128 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:13:13:0:3:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 11782 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:14:14:0:4:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 12070 . C T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:11:0:11:0:0:8:3:PASS +gi|9626243|ref|NC_001416.1| 12717 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:18:0:13:5:0:0:PASS +gi|9626243|ref|NC_001416.1| 12795 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:16:15:1:7:8:1:0:PASS +gi|9626243|ref|NC_001416.1| 12876 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:20:1:12:8:1:0:PASS +gi|9626243|ref|NC_001416.1| 12959 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:27:27:0:13:14:0:0:PASS +gi|9626243|ref|NC_001416.1| 12970 . A G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:26:0:26:0:0:14:12:PASS +gi|9626243|ref|NC_001416.1| 13107 . C A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:16:0:16:0:0:11:5:PASS +gi|9626243|ref|NC_001416.1| 13264 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:10:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 13542 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:19:0:12:7:0:0:PASS +gi|9626243|ref|NC_001416.1| 13647 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:20:5:0:0:PASS +gi|9626243|ref|NC_001416.1| 13952 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:20:19:1:8:11:1:0:PASS +gi|9626243|ref|NC_001416.1| 13971 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:27:0:27:0:0:12:15:PASS +gi|9626243|ref|NC_001416.1| 15384 . T G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:24:0:24:0:0:15:9:PASS +gi|9626243|ref|NC_001416.1| 15715 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:13:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 15967 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:11:14:0:0:PASS +gi|9626243|ref|NC_001416.1| 16070 . C A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:22:0:21:0:0:14:7:PASS +gi|9626243|ref|NC_001416.1| 16654 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:10:10:0:4:6:0:0:PASS +gi|9626243|ref|NC_001416.1| 16715 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:17:17:0:11:6:0:0:PASS +gi|9626243|ref|NC_001416.1| 17142 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:9:15:0:0:PASS +gi|9626243|ref|NC_001416.1| 17311 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:20:20:0:11:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 17854 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:20:20:0:10:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 18151 . A T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:22:0:22:0:0:11:11:PASS +gi|9626243|ref|NC_001416.1| 18188 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:20:19:1:9:10:0:1:PASS +gi|9626243|ref|NC_001416.1| 18210 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:11:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 18420 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:31:31:0:18:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 18598 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:17:17:0:11:6:0:0:PASS +gi|9626243|ref|NC_001416.1| 18652 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:17:17:0:8:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 18989 . G T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:30:0:30:0:0:13:17:PASS +gi|9626243|ref|NC_001416.1| 19208 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:31:31:0:16:15:0:0:PASS +gi|9626243|ref|NC_001416.1| 19448 . C A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:20:1:19:1:0:7:12:PASS +gi|9626243|ref|NC_001416.1| 19469 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:24:2:11:13:1:1:PASS +gi|9626243|ref|NC_001416.1| 20079 . C G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:36:0:36:0:0:19:17:PASS +gi|9626243|ref|NC_001416.1| 20099 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:13:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 20289 . T A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:23:0:23:0:0:7:16:PASS +gi|9626243|ref|NC_001416.1| 20367 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:12:14:0:0:PASS +gi|9626243|ref|NC_001416.1| 21110 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:12:12:0:1:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 21320 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:8:8:0:8:0:0:0:PASS +gi|9626243|ref|NC_001416.1| 21653 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:22:0:22:0:0:16:6:PASS +gi|9626243|ref|NC_001416.1| 22220 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:20:1:11:9:0:1:PASS +gi|9626243|ref|NC_001416.1| 22357 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:6:16:0:0:PASS +gi|9626243|ref|NC_001416.1| 22747 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:15:15:0:6:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 23362 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:4:4:0:0:4:0:0:PASS +gi|9626243|ref|NC_001416.1| 23457 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:10:10:0:10:0:0:0:PASS +gi|9626243|ref|NC_001416.1| 24043 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:13:8:0:0:PASS +gi|9626243|ref|NC_001416.1| 24319 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:27:26:1:13:13:0:1:PASS +gi|9626243|ref|NC_001416.1| 24766 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:19:0:6:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 24930 . A C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:26:0:26:0:0:12:14:PASS +gi|9626243|ref|NC_001416.1| 25005 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:10:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 25158 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:15:15:0:10:5:0:0:PASS +gi|9626243|ref|NC_001416.1| 25645 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:10:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 26173 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:31:28:3:10:18:2:1:PASS +gi|9626243|ref|NC_001416.1| 26728 . A T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:25:0:0:13:12:PASS +gi|9626243|ref|NC_001416.1| 26972 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:30:30:0:14:16:0:0:PASS +gi|9626243|ref|NC_001416.1| 27412 . C G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:15:0:15:0:0:6:9:PASS +gi|9626243|ref|NC_001416.1| 27539 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:15:15:0:11:4:0:0:PASS +gi|9626243|ref|NC_001416.1| 27661 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:15:15:0:7:8:0:0:PASS +gi|9626243|ref|NC_001416.1| 27722 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:18:1:6:12:1:0:PASS +gi|9626243|ref|NC_001416.1| 27790 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:11:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 27825 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:14:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 27834 . C A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:16:0:15:0:0:10:5:PASS +gi|9626243|ref|NC_001416.1| 28045 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:29:29:0:14:15:0:0:PASS +gi|9626243|ref|NC_001416.1| 28362 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:8:15:0:0:PASS +gi|9626243|ref|NC_001416.1| 29265 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:3:2:1:2:0:0:1:PASS +gi|9626243|ref|NC_001416.1| 29411 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:18:0:10:8:0:0:PASS +gi|9626243|ref|NC_001416.1| 29435 . T A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:18:0:18:0:0:11:7:PASS +gi|9626243|ref|NC_001416.1| 29891 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:30:29:1:16:13:0:1:PASS +gi|9626243|ref|NC_001416.1| 30125 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:29:29:0:20:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 30757 . T A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:24:0:24:0:0:10:14:PASS +gi|9626243|ref|NC_001416.1| 30890 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:18:0:17:0:0:7:10:PASS +gi|9626243|ref|NC_001416.1| 31328 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:21:0:21:0:0:9:12:PASS +gi|9626243|ref|NC_001416.1| 31363 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:31:31:0:14:17:0:0:PASS +gi|9626243|ref|NC_001416.1| 31551 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:14:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 32086 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:17:17:0:10:7:0:0:PASS +gi|9626243|ref|NC_001416.1| 32660 . C A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:17:0:17:0:0:11:6:PASS +gi|9626243|ref|NC_001416.1| 33000 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:15:15:0:9:6:0:0:PASS +gi|9626243|ref|NC_001416.1| 33591 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:27:27:0:14:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 33612 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:14:8:0:0:PASS +gi|9626243|ref|NC_001416.1| 33865 . T G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:28:0:28:0:0:15:13:PASS +gi|9626243|ref|NC_001416.1| 34137 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:21:1:8:13:1:0:PASS +gi|9626243|ref|NC_001416.1| 34370 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:29:29:0:12:17:0:0:PASS +gi|9626243|ref|NC_001416.1| 34812 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:30:29:1:11:18:1:0:PASS +gi|9626243|ref|NC_001416.1| 34920 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:12:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 35148 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:31:30:1:15:15:0:1:PASS +gi|9626243|ref|NC_001416.1| 35802 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:28:0:28:0:0:13:15:PASS +gi|9626243|ref|NC_001416.1| 35907 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:11:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 36010 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:14:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 36169 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:15:0:15:0:0:5:10:PASS +gi|9626243|ref|NC_001416.1| 36642 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:18:1:10:8:1:0:PASS +gi|9626243|ref|NC_001416.1| 37208 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:13:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 37387 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:11:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 37519 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:13:0:13:0:0:6:7:PASS +gi|9626243|ref|NC_001416.1| 37898 . C G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:27:0:26:0:0:8:18:PASS +gi|9626243|ref|NC_001416.1| 38073 . A C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:24:0:0:17:7:PASS +gi|9626243|ref|NC_001416.1| 38165 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:17:16:1:11:5:0:1:PASS +gi|9626243|ref|NC_001416.1| 38575 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:14:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 39003 . T C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:17:0:17:0:0:9:8:PASS +gi|9626243|ref|NC_001416.1| 39206 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:20:20:0:8:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 39484 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:20:20:0:7:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 39485 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:16:16:0:4:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 40457 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:24:1:7:17:1:0:PASS +gi|9626243|ref|NC_001416.1| 40835 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:28:28:0:17:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 40984 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:37:36:1:20:16:0:1:PASS +gi|9626243|ref|NC_001416.1| 41064 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:30:30:0:15:15:0:0:PASS +gi|9626243|ref|NC_001416.1| 41448 . A G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:21:0:21:0:0:8:13:PASS +gi|9626243|ref|NC_001416.1| 41954 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:20:19:1:6:13:1:0:PASS +gi|9626243|ref|NC_001416.1| 42439 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:20:20:0:11:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 43306 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:6:17:0:0:PASS +gi|9626243|ref|NC_001416.1| 43470 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:14:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 44134 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:20:20:0:10:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 44201 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:16:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 44413 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:9:14:0:0:PASS +gi|9626243|ref|NC_001416.1| 45364 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:29:28:1:13:15:1:0:PASS +gi|9626243|ref|NC_001416.1| 45409 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:27:27:0:16:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 46237 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:17:16:1:8:8:0:1:PASS +gi|9626243|ref|NC_001416.1| 46283 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:11:14:0:0:PASS +gi|9626243|ref|NC_001416.1| 46842 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:28:0:27:0:0:17:10:PASS +gi|9626243|ref|NC_001416.1| 47425 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:12:11:1:11:0:1:0:PASS +gi|9626243|ref|NC_001416.1| 47893 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:27:27:0:12:15:0:0:PASS
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samples/sample4/consensus.vcf Wed Nov 22 15:34:14 2023 +0000 @@ -0,0 +1,186 @@ +##fileformat=VCFv4.1 +##fileDate=20180103 +##source=CFSAN SNP-Pipeline 1.0.1 +##reference=lambda_virus.fasta +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw read depth"> +##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)"> +##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)"> +##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)"> +##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)"> +##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)"> +##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)"> +##FORMAT=<ID=FT,Number=1,Type=String,Description="Genotype filters using the same codes as the FILTER data element"> +##FILTER=<ID=PASS,Description="All filters passed"> +##FILTER=<ID=RawDpth,Description="No read depth"> +##FILTER=<ID=VarFreq60,Description="Variant base frequency below 0.60"> +##FILTER=<ID=StrDpth0,Description="Less than 0 variant-supporing reads on at least one strand"> +##FILTER=<ID=StrBias0,Description="Fraction of variant supporting reads below 0.00 on one strand"> +##FILTER=<ID=Region,Description="Position is in dense region of snps or near the end of the contig."> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample4 +gi|9626243|ref|NC_001416.1| 403 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:15:15:0:11:4:0:0:PASS +gi|9626243|ref|NC_001416.1| 550 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:26:0:26:0:0:14:12:PASS +gi|9626243|ref|NC_001416.1| 586 . C G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:27:0:25:0:0:17:8:PASS +gi|9626243|ref|NC_001416.1| 753 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:12:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 1019 . C T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:22:0:22:0:0:8:14:PASS +gi|9626243|ref|NC_001416.1| 1079 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:27:27:0:11:16:0:0:PASS +gi|9626243|ref|NC_001416.1| 1540 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:28:28:0:14:14:0:0:PASS +gi|9626243|ref|NC_001416.1| 1620 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:19:0:19:0:0:7:12:PASS +gi|9626243|ref|NC_001416.1| 1650 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:26:0:26:0:0:10:16:PASS +gi|9626243|ref|NC_001416.1| 1788 . A T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:16:0:16:0:0:9:7:PASS +gi|9626243|ref|NC_001416.1| 1804 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:18:0:7:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 2123 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:28:28:0:13:15:0:0:PASS +gi|9626243|ref|NC_001416.1| 2439 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:27:27:0:10:17:0:0:PASS +gi|9626243|ref|NC_001416.1| 2452 . A T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:23:1:22:1:0:13:9:PASS +gi|9626243|ref|NC_001416.1| 2599 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:19:0:8:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 3063 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:22:0:21:0:0:10:11:PASS +gi|9626243|ref|NC_001416.1| 3351 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:10:14:0:0:PASS +gi|9626243|ref|NC_001416.1| 3648 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:10:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 3656 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:28:28:0:18:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 3678 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:11:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 4977 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:27:26:1:14:12:0:1:PASS +gi|9626243|ref|NC_001416.1| 5142 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:9:16:0:0:PASS +gi|9626243|ref|NC_001416.1| 5336 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:33:33:0:11:22:0:0:PASS +gi|9626243|ref|NC_001416.1| 5462 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:32:32:0:10:22:0:0:PASS +gi|9626243|ref|NC_001416.1| 5482 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:25:1:13:12:0:1:PASS +gi|9626243|ref|NC_001416.1| 5516 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:23:2:13:10:0:2:PASS +gi|9626243|ref|NC_001416.1| 5800 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:18:0:10:8:0:0:PASS +gi|9626243|ref|NC_001416.1| 5818 . G T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:23:0:22:0:0:11:11:PASS +gi|9626243|ref|NC_001416.1| 5994 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:15:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 6296 . T A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:26:0:25:0:0:13:12:PASS +gi|9626243|ref|NC_001416.1| 6535 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:27:27:0:13:14:0:0:PASS +gi|9626243|ref|NC_001416.1| 6824 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:12:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 7424 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:6:6:0:0:6:0:0:PASS +gi|9626243|ref|NC_001416.1| 7668 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:14:14:0:10:4:0:0:PASS +gi|9626243|ref|NC_001416.1| 7897 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:11:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 8420 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:12:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 8938 . T A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:29:0:29:0:0:17:12:PASS +gi|9626243|ref|NC_001416.1| 9175 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:31:31:0:13:18:0:0:PASS +gi|9626243|ref|NC_001416.1| 9234 . C T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:21:0:21:0:0:10:11:PASS +gi|9626243|ref|NC_001416.1| 9919 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:11:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 10127 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:12:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 10264 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:18:0:14:4:0:0:PASS +gi|9626243|ref|NC_001416.1| 10421 . G T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:18:0:18:0:0:8:10:PASS +gi|9626243|ref|NC_001416.1| 10568 . C T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:21:0:21:0:0:10:11:PASS +gi|9626243|ref|NC_001416.1| 11066 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:27:26:1:9:17:0:1:PASS +gi|9626243|ref|NC_001416.1| 11128 . T A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:25:0:0:10:15:PASS +gi|9626243|ref|NC_001416.1| 11782 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:11:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 12070 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:18:0:12:6:0:0:PASS +gi|9626243|ref|NC_001416.1| 12717 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:20:19:1:7:12:1:0:PASS +gi|9626243|ref|NC_001416.1| 12795 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:15:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 12876 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:19:0:19:0:0:7:12:PASS +gi|9626243|ref|NC_001416.1| 12959 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:21:2:10:11:2:0:PASS +gi|9626243|ref|NC_001416.1| 12970 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:13:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 13107 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:21:1:8:13:0:1:PASS +gi|9626243|ref|NC_001416.1| 13264 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:12:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 13542 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:13:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 13647 . C T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:17:0:17:0:0:11:6:PASS +gi|9626243|ref|NC_001416.1| 13952 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:33:33:0:12:21:0:0:PASS +gi|9626243|ref|NC_001416.1| 13971 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:30:29:1:11:18:0:1:PASS +gi|9626243|ref|NC_001416.1| 15384 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:14:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 15715 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:8:15:0:0:PASS +gi|9626243|ref|NC_001416.1| 15967 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:29:28:1:14:14:1:0:PASS +gi|9626243|ref|NC_001416.1| 16070 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:24:1:11:13:0:1:PASS +gi|9626243|ref|NC_001416.1| 16654 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:10:15:0:0:PASS +gi|9626243|ref|NC_001416.1| 16715 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:20:20:0:6:14:0:0:PASS +gi|9626243|ref|NC_001416.1| 17142 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:15:15:0:6:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 17311 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:10:10:0:1:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 17854 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:36:34:2:18:16:0:2:PASS +gi|9626243|ref|NC_001416.1| 18151 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:14:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 18188 . T C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:31:0:31:0:0:17:14:PASS +gi|9626243|ref|NC_001416.1| 18210 . C G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:29:0:29:0:0:15:14:PASS +gi|9626243|ref|NC_001416.1| 18420 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:17:17:0:6:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 18598 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:20:20:0:12:8:0:0:PASS +gi|9626243|ref|NC_001416.1| 18652 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:12:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 18989 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:7:14:0:0:PASS +gi|9626243|ref|NC_001416.1| 19208 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:31:30:1:15:15:0:1:PASS +gi|9626243|ref|NC_001416.1| 19448 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:33:33:0:21:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 19469 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:31:31:0:17:14:0:0:PASS +gi|9626243|ref|NC_001416.1| 20079 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:32:32:0:17:15:0:0:PASS +gi|9626243|ref|NC_001416.1| 20099 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:10:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 20289 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:29:28:1:13:15:1:0:PASS +gi|9626243|ref|NC_001416.1| 20367 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:10:16:0:0:PASS +gi|9626243|ref|NC_001416.1| 21110 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:16:16:0:9:7:0:0:PASS +gi|9626243|ref|NC_001416.1| 21320 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:9:16:0:0:PASS +gi|9626243|ref|NC_001416.1| 21653 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:19:0:10:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 22220 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:22:1:8:14:0:1:PASS +gi|9626243|ref|NC_001416.1| 22357 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:21:0:21:0:0:11:10:PASS +gi|9626243|ref|NC_001416.1| 22747 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:8:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 23362 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:11:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 23457 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:25:1:12:13:1:0:PASS +gi|9626243|ref|NC_001416.1| 24043 . C A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:15:0:15:0:0:7:8:PASS +gi|9626243|ref|NC_001416.1| 24319 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:11:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 24766 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:14:14:0:5:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 24930 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:10:9:1:4:5:1:0:PASS +gi|9626243|ref|NC_001416.1| 25005 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:16:16:0:10:6:0:0:PASS +gi|9626243|ref|NC_001416.1| 25158 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:20:1:12:8:0:1:PASS +gi|9626243|ref|NC_001416.1| 25645 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:13:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 26173 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:11:14:0:0:PASS +gi|9626243|ref|NC_001416.1| 26728 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:9:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 26972 . A T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:22:1:21:1:0:11:10:PASS +gi|9626243|ref|NC_001416.1| 27412 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:15:15:0:7:8:0:0:PASS +gi|9626243|ref|NC_001416.1| 27539 . A C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:11:0:11:0:0:5:6:PASS +gi|9626243|ref|NC_001416.1| 27661 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:18:0:10:8:0:0:PASS +gi|9626243|ref|NC_001416.1| 27722 . C A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:26:0:26:0:0:16:10:PASS +gi|9626243|ref|NC_001416.1| 27790 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:19:0:14:5:0:0:PASS +gi|9626243|ref|NC_001416.1| 27825 . A G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:22:0:22:0:0:14:8:PASS +gi|9626243|ref|NC_001416.1| 27834 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:20:1:11:9:1:0:PASS +gi|9626243|ref|NC_001416.1| 28045 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:18:0:9:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 28362 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:13:13:0:13:0:0:0:PASS +gi|9626243|ref|NC_001416.1| 29265 . T C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:28:0:27:0:0:9:18:PASS +gi|9626243|ref|NC_001416.1| 29411 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:36:35:1:17:18:1:0:PASS +gi|9626243|ref|NC_001416.1| 29435 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:32:31:1:15:16:1:0:PASS +gi|9626243|ref|NC_001416.1| 29891 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:29:28:1:15:13:1:0:PASS +gi|9626243|ref|NC_001416.1| 30125 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:31:29:2:11:18:1:1:PASS +gi|9626243|ref|NC_001416.1| 30757 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:28:28:0:13:15:0:0:PASS +gi|9626243|ref|NC_001416.1| 30890 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:11:13:0:0:PASS +gi|9626243|ref|NC_001416.1| 31328 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:9:9:0:9:0:0:0:PASS +gi|9626243|ref|NC_001416.1| 31363 . C G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:9:0:9:0:0:8:1:PASS +gi|9626243|ref|NC_001416.1| 31551 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:14:7:0:0:PASS +gi|9626243|ref|NC_001416.1| 32086 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:19:0:10:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 32660 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:23:1:12:11:1:0:PASS +gi|9626243|ref|NC_001416.1| 33000 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:27:26:1:12:14:0:1:PASS +gi|9626243|ref|NC_001416.1| 33591 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:19:0:9:10:0:0:PASS +gi|9626243|ref|NC_001416.1| 33612 . C A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:19:0:18:0:0:7:11:PASS +gi|9626243|ref|NC_001416.1| 33865 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:12:9:0:0:PASS +gi|9626243|ref|NC_001416.1| 34137 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:13:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 34370 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:32:31:1:15:16:1:0:PASS +gi|9626243|ref|NC_001416.1| 34812 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:31:31:0:12:19:0:0:PASS +gi|9626243|ref|NC_001416.1| 34920 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:6:16:0:0:PASS +gi|9626243|ref|NC_001416.1| 35148 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:17:17:0:11:6:0:0:PASS +gi|9626243|ref|NC_001416.1| 35802 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:7:14:0:0:PASS +gi|9626243|ref|NC_001416.1| 35907 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:18:1:12:6:0:1:PASS +gi|9626243|ref|NC_001416.1| 36010 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:11:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 36169 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:28:28:0:10:18:0:0:PASS +gi|9626243|ref|NC_001416.1| 36642 . T C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:17:0:17:0:0:2:15:PASS +gi|9626243|ref|NC_001416.1| 37208 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:14:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 37387 . A T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:15:0:15:0:0:7:8:PASS +gi|9626243|ref|NC_001416.1| 37519 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:18:1:12:6:1:0:PASS +gi|9626243|ref|NC_001416.1| 37898 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:16:15:1:11:4:0:1:PASS +gi|9626243|ref|NC_001416.1| 38073 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:14:14:0:9:5:0:0:PASS +gi|9626243|ref|NC_001416.1| 38165 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:18:0:7:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 38575 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:23:1:16:7:0:1:PASS +gi|9626243|ref|NC_001416.1| 39003 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:14:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 39206 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:11:14:0:0:PASS +gi|9626243|ref|NC_001416.1| 39484 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:10:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 39485 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:19:0:7:12:0:0:PASS +gi|9626243|ref|NC_001416.1| 40457 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:30:30:0:15:15:0:0:PASS +gi|9626243|ref|NC_001416.1| 40835 . T C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:25:0:0:16:9:PASS +gi|9626243|ref|NC_001416.1| 40984 . A G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:22:0:21:0:0:12:9:PASS +gi|9626243|ref|NC_001416.1| 41064 . T G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:22:0:21:0:0:10:11:PASS +gi|9626243|ref|NC_001416.1| 41448 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:18:1:9:9:1:0:PASS +gi|9626243|ref|NC_001416.1| 41954 . T C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:23:0:23:0:0:11:12:PASS +gi|9626243|ref|NC_001416.1| 42439 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:11:14:0:0:PASS +gi|9626243|ref|NC_001416.1| 43306 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:28:28:0:10:18:0:0:PASS +gi|9626243|ref|NC_001416.1| 43470 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:27:26:1:17:9:0:1:PASS +gi|9626243|ref|NC_001416.1| 44134 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:27:26:1:13:13:0:1:PASS +gi|9626243|ref|NC_001416.1| 44201 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:24:0:0:15:9:PASS +gi|9626243|ref|NC_001416.1| 44413 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:15:15:0:1:14:0:0:PASS +gi|9626243|ref|NC_001416.1| 45364 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:27:26:1:11:15:1:0:PASS +gi|9626243|ref|NC_001416.1| 45409 . C G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:21:0:21:0:0:8:13:PASS +gi|9626243|ref|NC_001416.1| 46237 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:28:26:2:10:16:0:2:PASS +gi|9626243|ref|NC_001416.1| 46283 . C G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:22:0:22:0:0:11:11:PASS +gi|9626243|ref|NC_001416.1| 46842 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:10:15:0:0:PASS +gi|9626243|ref|NC_001416.1| 47425 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:12:11:0:0:PASS +gi|9626243|ref|NC_001416.1| 47893 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:11:11:0:0:PASS